How Can We Advance Integrative Biology Research in Animal Science in 21st Century? Experience at University of Ljubljana from 2002 to 2022.

In this perspective analysis, we strive to answer the following question: how can we advance integrative biology research in the 21st century with lessons from animal science? At the University of Ljubljana, Biotechnical Faculty, Department of Animal Science, we share here our three lessons learned in the two decades from 2002 to 2022 that we believe could inform integrative biology, systems science, and animal science scholarship in other countries and geographies. Cultivating multiomics knowledge through a conceptual lens of integrative biology is crucial for life sciences research that can stand the test of diverse biological, clinical, and ecological contexts. Moreover, in an era of the current COVID-19 pandemic, animal nutrition and animal science, and the study of their interactions with human health (and vice versa) through integrative biology approaches hold enormous prospects and significance for systems medicine and ecosystem health.

Influence of support materials on continuous hydrogen production in anaerobic packed-bed reactor with immobilized hydrogen producing bacteria at acidic conditions.

This study assesses the impact of different support materials (Mutag BioChip™, expanded clay and activated carbon) on microbial hydrogen production in an anaerobic packed-bed reactor (APBR) treating synthetic waste water containing glucose as the main carbon source at low pH value. The APBRs were inoculated with acid pretreated anaerobic sludge and operated at pH value of 4±0.2 and hydraulic retention time (HRT) of 3h.

Influence of Thermal and Bacterial Pretreatment of Microalgae on Biogas Production in Mesophilic and Thermophilic Conditions.

Microalgae biomass has a great potential in search for new alternative energy sources. They can be used as a substrate for the biogas production in anaerobic digestion. When using microalgae, the efficiency of this process is hampered due to the resistant cell wall.

Thermal pretreatment and bioaugmentation improve methane yield of microalgal mix produced in thermophilic anaerobic digestate.

Liquid fraction produced in anaerobic digestion (AD) of biodegradable waste can be treated on-site with microalgae, which can be recycled back as substrate to the biogas plant. For this research, a pilot high rate algal pond (HRAP) was set with connections to a full scale biogas plant that enabled the use of waste heat and CO from a combined heat and power gen-set (CHP). The microalgal mix produced in the thermophilic anaerobic digestate supernatant was tested as a substrate for biogas production in the thermophilic AD (i.

Biogas production from brewery spent grain enhanced by bioaugmentation with hydrolytic anaerobic bacteria.

Lignocellulosic substrates are widely available but not easily applied in biogas production due to their poor anaerobic degradation. The effect of bioaugmentation by anaerobic hydrolytic bacteria on biogas production was determined by the biochemical methane potential assay. Microbial biomass from full scale upflow anaerobic sludge blanket reactor treating brewery wastewater was a source of active microorganisms and brewery spent grain a model lignocellulosic substrate.

Identification of GH10 xylanases in strains 2 and Mz5 of Pseudobutyrivibrio xylanivorans.

Genes encoding glycosyl hydrolase family 11 (GH11) xylanases and xylanases have been identified from Pseudobutyrivibrio xylanivorans. In contrast, little is known about the diversity and distribution of the GH10 xylanase in strains of P. xylanivorans.

Microbial community analyses in biogas reactors by molecular methods.

Successful biogas production is based on stable or adaptable microbial community structure and activity which depends on type of substrate used and several physico-chemical conditions in the bioreactor. Monitoring those and the dynamics of microbiota is important for planning and optimizing the biogas process, avoiding critical points and reaching the maximum methane yield. Methanogens are extremely difficult to study with culture-based methods.

Expression of cellulosome components and type IV pili within the extracellular proteome of Ruminococcus flavefaciens 007.

Background: Ruminococcus flavefaciens is an important fibre-degrading bacterium found in the mammalian gut. Cellulolytic strains from the bovine rumen have been shown to produce complex cellulosome structures that are associated with the cell surface. R.

Biotic and abiotic processes contribute to successful anaerobic degradation of cyanide by UASB reactor biomass treating brewery waste water.

In contrast to the general aerobic detoxification of industrial effluents containing cyanide, anaerobic cyanide degradation is not well understood, including the microbial communities involved. To address this knowledge gap, this study measured anaerobic cyanide degradation and the rearrangements in bacterial and archaeal microbial communities in an upflow anaerobic sludge blanket (UASB) reactor biomass treating brewery waste water using bio-methane potential assays, molecular profiling, sequencing and microarray approaches. Successful biogas formation and cyanide removal without inhibition were observed at cyanide concentrations up to 5 mg l(-1).

The effects of engineered nanoparticles on the cellular structure and growth of Saccharomyces cerevisiae.

In order to study the effects of nanoparticles (NPs) with different physicochemical properties on cellular viability and structure, Saccharomyces cerevisiae were exposed to different concentrations of TiO2-NPs (1-3 nm), ZnO-NPs (<100 nm), CuO-NPs (<50 nm), their bulk forms, Ag-NPs (10 nm) and single-walled carbon nanotubes (SWCNTs). The GreenScreen assay was used to measure cyto- and genotoxicity, and transmission electron microscopy (TEM) used to assess ultrastructure. CuO-NPs were highly cytotoxic, reducing the cell density by 80% at 9 cm(2)/ml, and inducing lipid droplet formation.

Anaerobic co-digestion of excess brewery yeast in a granular biomass reactor to enhance the production of biomethane.

The anaerobic co-digestion of brewery yeast using granular biomass was studied on the lab, pilot and full-scale. The study shows no adverse effects in the co-digestion of yeast and wastewater in concentrations up to 1.1 (v/v)%.

Experimental evidence of false-positive Comet test results due to TiO2 particle--assay interactions.

We have studied the genotoxicity of TiO2 particles with a Comet assay on a unicellular organism, Tetrahymena thermophila. Exposure to bulk- or nano-TiO2 of free cells, cells embedded in gel or nuclei embedded in gel, all resulted in a positive Comet assay result but this outcome could not be confirmed by cytotoxicity measures such as lipid peroxidation, elevated reactive oxygen species or cell membrane composition. Published reports state that in the absence of cytotoxicity, nano- and bulk-TiO2 genotoxicity do not occur directly, and a possible explanation of our Comet assay results is that they are false positives resulting from post festum exposure interactions between particles and DNA.

Expression patterns of Ruminococcus flavefaciens 007S cellulases as revealed by zymogram approach.

The expression of Ruminococcus flavefaciens 007S cellulases in different incubation time points (growth stages) and their substrate inducibility were analyzed by comparing the zymogram expression profiles of cultures grown on insoluble cellulose (Avicel) with cellobiose-grown cultures. The molecular weights of the enzymes were compared to (putative) cellulases encoded in the R. flavefaciens FD-1 genome.

Exposure to Al2O3 nanoparticles changes the fatty acid profile of the anaerobe Ruminococcus flavefaciens.

One of the main mechanisms of nanoparticle toxicity is known to be the generation of reactive oxygen species (ROS) which primarily damage cell membranes. However, very limited data on membrane effects in anaerobic environments (where ROS could not be the cause of membrane damage) are available. In the following study, rumen anaerobe Ruminococcus flavefaciens 007C was used as a bacterial model to assess the potential effects of Al(2)O(3) and TiO(2) nanoparticles on membranes in an anaerobic environment.

Membrane Changes Associated with Exposure of Pseudomonas putida to Selected Environmental Pollutants and their Possible Roles in Toxicity.

A bacterial model system (Pseudomonas putida DSM 50026) was used in this research to assess potential effect of five selected chemically diverse environmental pollutants on cell membranes. Long chain fatty acid profiles of cultures exposed to environmentally relevant concentrations of atrazine (ATR), metolachlor (MET), pentachlorobiphenyl (PCB), hexachlorobenzene (HCB) and fluoranthene (FL), were analyzed and compared to non-exposed cultures. To assess sensitivity of membrane-based responses, the impact of each toxicant on culture growth was also followed spectrophotometrically.

Exposure to CuO nanoparticles changes the fatty acid composition of protozoa Tetrahymena thermophila.

In the current study, the toxicity mechanism of nanosized CuO (nCuO) to the freshwater ciliated protozoa Tetrahymena thermophila was studied. Changes in fatty acid profile, lipid peroxidation metabolites and reactive oxygen species (ROS) were measured. Bulk CuO and CuSO(4) served as controls for size and solubility and 3,5-dichorophenol (3,5-DCP) as a control for a chemical known to directly affect the membrane composition.

General Microbial Community Flexibility in Biochemical Methane Potential Assay is Highly Correlated to Initial Biogas Production Rates.

Degradation of brewery spent grain as a novel test substrate was explored in routine biochemical methane potential assays (BMP) using three different inocula. Significant differences in the initial biogas production rates from spent grain, methane yield coefficients and final spent grain degradation were observed between inocula. Initial and developed communities degrading novel substrate showed significant differences in archaeal community fingerprints.

Anaerobic digestion of brewery spent grain in a semi-continuous bioreactor: inhibition by phenolic degradation products.

In this study anaerobic digestion of selected lignocellulosic substrate, namely brewery spent grain (BSG), was studied. In order to facilitate anaerobic digestion several types of pretreatment methods were tested such as: mechanical, chemical (alkali and acid) and thermo-chemical. The anaerobic digestion experiments were carried out in a semi-continuous stirred bioreactors with the organic loading rates between 2.

Cellulosomes - promising supramolecular machines of anaerobic cellulolytic microorganisms.

Cellulose is the main structural component of plant cell wall and thus the most abundant carbohydrate in nature. However, extracting the energy from this abundant source is limited by its recalcitrant nature. The hydrolysis of plant cell wall requires synergystic action of different enzymes, including multiple cellulases, hemicellulases, pectinases, etc.

Conditioning of the membrane fatty acid profile of Escherichia coli during periodic temperature cycling.

The membrane fatty acid composition of Escherichia coli becomes conditioned during periodic temperature cycling between 37 and 8 degrees C. After several cycles of temperature change, the bacteria become locked into a low-temperature physiology. Even after a prolonged incubation at high temperature the membrane fatty acid composition of conditioned cells was similar to that of cold-stressed cells.

Bioassays for evaluating the water-extractable genotoxic and toxic potential of soils polluted by metal smelters.

Physicochemical analyses of polluted soils are limited in their ability to determine all hazardous compounds, their bioavailability, and their combined effects on living organisms. Bioassays, on the other hand, can evaluate environmental quality more accurately. This study assesses the genotoxic potential of water extracts from soil polluted with metals (Pb, Cd, and Zn) by the former lead smelter in zerjav, Slovenia using comet assay with Tetrahymena thermophila and human hepatoma cells (HepG2).

Genotoxicity evaluation of water soil leachates by Ames test, comet assay, and preliminary Tradescantia micronucleus assay.

Combining genotoxicity/mutagenicity tests and physico-chemical methodologies can be useful for determining the potential genotoxic contaminants in soil samples. The aim of our study was to evaluate the genotoxicity of soil by applying an integrated physico-chemical-biological approach. Soil samples were collected at six sampling points in a Slovenian industrial and agricultural region where contamination by heavy metals and sulphur dioxide (SO(2)) are primarily caused by a nearby power plant.

Butyrivibrio hungatei sp. nov. and Pseudobutyrivibrio xylanivorans sp. nov., butyrate-producing bacteria from the rumen.

Two novel Gram-negative, anaerobic, non-spore-forming, butyrate-producing bacterial species, strains Mz 5T and JK 615T, were isolated from the rumen fluid of cow and sheep. Both strains were curved rods that were motile by means of single polar or subpolar flagellum and common in the rumen microbial ecosystem. Strain Mz 5T produced high xylanase, proteinase, pectin hydrolase and DNase activities; 1,4-beta-endoglucanase was also detected in the culture medium.